def plot_enc_convergence(directory="../vasp/examples/SiOptb88/",
plot=False,
filename="."):
"""
Plot convergence for plane-wave cut-off data
Works only if jobs run through jarvis-tools framework
Args:
directory: parent directory for job run
Returns:
matplotlib object, converged cut-off value
"""
x = []
y = []
for a in glob.glob(str(directory) + str("/*.json")):
if "MAIN-RELAX" in a:
main_inc = str(a.split(".json")[0]) + str("/") + str("INCAR")
main_inc_obj = Incar.from_file(main_inc)
convg_encut = float(main_inc_obj["ENCUT"])
elif "ENCUT" in a:
run = str(a.split(".json")[0]) + str("/") + str("vasprun.xml")
contcar = Structure.from_file((a.split(".json")[0]) + str("/") +
str("CONTCAR"))
vrun = Vasprun(run)
infile = str(a.split(".json")[0]) + str("/") + str("INCAR")
inc = Incar.from_file(infile)
encut = inc["ENCUT"]
en = float(
vrun.final_energy) # /float(contcar.composition.num_atoms)
x.append(encut)
y.append(en)
order = np.argsort(x)
xs = np.array(x)[order]
ys = np.array(y)[order]
plt = get_publication_quality_plot(14, 10)
plt.ylabel("Energy (eV)")
plt.plot(xs, ys, "s-", linewidth=2, markersize=10)
plt.xlabel("Increment in ENCUT ")
ax = plt.gca()
ax.get_yaxis().get_major_formatter().set_useOffset(False)
plt.title(str("Converged at ") + str(int(convg_encut)) + str("eV"),
fontsize=26)
# filename=str('Encut.png')
plt.tight_layout()
if plot == True:
plt.savefig(filename)
plt.close()
return plt, convg_encut
def plot(self, ax=None):
"""Plots the simulated electron diffraction pattern with a logarithmic
intensity scale.
Run `.show()` on the result of this method to display the plot.
Parameters
----------
ax : :obj:`matplotlib.axes.Axes`, optional
A `matplotlib` axes instance. Used if the plot needs to be in a
figure that has been created elsewhere.
"""
if ax is None:
plt = get_publication_quality_plot(10, 10)
ax = plt.gca()
ax.scatter(self.coordinates[:, 0],
self.coordinates[:, 1],
s=np.log10(self.intensities))
ax.set_xlabel("Reciprocal Dimension ($A^{-1}$)")
ax.set_ylabel("Reciprocal Dimension ($A^{-1}$)")
return ax
def bandstr(vrun="", kpfile="", filename=".", plot=False):
"""
Plot electronic bandstructure
Args:
vrun: path to vasprun.xml
kpfile:path to line mode KPOINTS file
Returns:
matplotlib object
"""
run = Vasprun(vrun, parse_projected_eigen=True)
bands = run.get_band_structure(kpfile, line_mode=True, efermi=run.efermi)
bsp = BSPlotter(bands)
zero_to_efermi = True
bandgap = str(round(bands.get_band_gap()["energy"], 3))
# print "bg=",bandgap
data = bsp.bs_plot_data(zero_to_efermi)
plt = get_publication_quality_plot(12, 8)
plt.close()
plt.clf()
band_linewidth = 3
x_max = data["distances"][-1][-1]
# print (x_max)
for d in range(len(data["distances"])):
for i in range(bsp._nb_bands):
plt.plot(
data["distances"][d],
[
data["energy"][d]["1"][i][j]
for j in range(len(data["distances"][d]))
],
"b-",
linewidth=band_linewidth,
)
if bsp._bs.is_spin_polarized:
plt.plot(
data["distances"][d],
[
data["energy"][d]["-1"][i][j]
for j in range(len(data["distances"][d]))
],
"r--",
linewidth=band_linewidth,
)
bsp._maketicks(plt)
if bsp._bs.is_metal():
e_min = -10
e_max = 10
band_linewidth = 3
for cbm in data["cbm"]:
plt.scatter(cbm[0], cbm[1], color="r", marker="o", s=100)
for vbm in data["vbm"]:
plt.scatter(vbm[0], vbm[1], color="g", marker="o", s=100)
plt.xlabel(r"$\mathrm{Wave\ Vector}$", fontsize=30)
ylabel = (
r"$\mathrm{E\ -\ E_f\ (eV)}$" if zero_to_efermi else r"$\mathrm{Energy\ (eV)}$"
)
plt.ylabel(ylabel, fontsize=30)
plt.ylim(-4, 4)
plt.xlim(0, x_max)
plt.tight_layout()
if plot == True:
plt.savefig(filename, img_format="png")
plt.close()
return plt
def plot_kp_convergence(
directory="../vasp/examples/SiOptb88/", plot=False, filename="."
):
"""
Plot convergence for k-points data
Works only if jobs run through jarvis-tools framework
Args:
directory: parent directory for job run
Returns:
matplotlib object, converged k-points value
"""
x = []
y = []
for a in glob.glob(str(directory) + str("/*.json")):
if "MAIN-RELAX" in a:
main_kp = str(a.split(".json")[0]) + str("/") + str("KPOINTS")
main_kp_obj = Kpoints.from_file(main_kp)
[k1, k2, k3] = main_kp_obj.kpts[0]
elif "KPOINT" in a:
k = int(float(str(a.split("-")[-1]).split(".json")[0]))
run = str(a.split(".json")[0]) + str("/") + str("vasprun.xml")
vrun = Vasprun(run)
kpfile = str(a.split(".json")[0]) + str("/") + str("KPOINTS")
contcar = Structure.from_file(
(a.split(".json")[0]) + str("/") + str("CONTCAR")
)
kpoints = Kpoints.from_file(kpfile)
[xx, yy, zz] = kpoints.kpts[0]
en = float(vrun.final_energy) # /float(contcar.composition.num_atoms)
# en =float(vrun.final_energy)/float(contcar.composition.num_atoms)
# print "ENERGYYY,AT",en,float(contcar.composition.num_atoms)
x.append(k)
y.append(en)
order = np.argsort(x)
xs = np.array(x)[order]
ys = np.array(y)[order]
len_xs = len(xs)
xs1 = []
ys1 = []
target_ys = ys[-1]
# print "target=",target_ys
for i, el in enumerate(ys):
if el <= (float(target_ys) + 0.002):
xs1.append(xs[i])
ys1.append(ys[i])
# print "xs,ys=",xs,ys
# print "xs1,ys1=",xs1,ys1
left, bottom, width, height = [0.5, 0.5, 0.35, 0.35]
plt = get_publication_quality_plot(14, 10)
fig, ax1 = plt.subplots()
plt.xlabel("Increment in K point", fontsize=20)
plt.ylabel("Energy (eV)", fontsize=20)
plt.title(
str("Converged at ")
+ str(k1)
+ str("x")
+ str(k2)
+ str("x")
+ str(k3)
+ str(" ")
+ str("Automatic Mesh ")
+ str(max(x) - 25),
fontsize=14,
)
plt.xticks(fontsize=20)
plt.yticks(fontsize=20)
ax2 = fig.add_axes([left, bottom, width, height])
# ax2.plot(xs1,ys1, '.-',linewidth=2,markersize=10)
ax1.plot(xs, ys, "s-", linewidth=2, markersize=10)
el_list = sorted(list(contcar.symbol_set))
search = "-".join([item for item in el_list])
# ax1.xlabel('Increment in K point')
# print "xs,ys"
# print xs
# print ys
plt.plot(xs1, ys1, ".-", linewidth=2, markersize=10)
plt.ylim([float(target_ys) + 0.002, float(target_ys) - 0.002])
ax = plt.gca()
ax.get_yaxis().get_major_formatter().set_useOffset(False)
filename = str("KDen.png")
k_convg = str(xx) + str("x") + str(yy) + str("x") + str(zz)
plt.tight_layout()
if plot == True:
plt.savefig(filename)
plt.close()
return plt, k_convg
def plot_dos(vrun="", low_lim=-5, up_lim=10, filename=".", extra="", plot=False):
"""
Plot total density of states
Args:
vrun: vasprun.xml path
low_lim: lower energy limit in eV
up_lim: upper energy limit in eV
Returns:
matplotlib objects for
total, orbital and element project density of states
"""
run = Vasprun(vrun, occu_tol=1e-2)
complete_dos = run.complete_dos
totup = complete_dos.get_densities(spin=Spin.up)
totdn = complete_dos.get_densities(spin=Spin.down)
en = complete_dos.energies
bandgap = str(run.eigenvalue_band_properties[0])
ef = complete_dos.efermi
en[:] = [x - ef for x in en]
plt1 = get_publication_quality_plot(14, 10)
# plt1.close()
# plt1.clf()
plt1.xlabel("Energies (eV)")
plt1.ylabel("Tot. DOS (arb. unit.)")
plt1.plot(en, totup, "b", linewidth=3)
plt1.plot(en, -totdn, "r", linewidth=3)
plt1.xlim(low_lim, up_lim)
plt1.tight_layout()
if plot == True:
tmp = str(filename) + str("/TDos") + str(extra) + str(".png")
plt1.savefig(tmp)
spd_dos = complete_dos.get_spd_dos()
sdosup = spd_dos[OrbitalType.s].densities[Spin.up]
pdosup = spd_dos[OrbitalType.p].densities[Spin.up]
ddosup = spd_dos[OrbitalType.d].densities[Spin.up]
sdosdn = spd_dos[OrbitalType.s].densities[Spin.down]
pdosdn = spd_dos[OrbitalType.p].densities[Spin.down]
ddosdn = spd_dos[OrbitalType.d].densities[Spin.down]
plt2 = get_publication_quality_plot(14, 10)
# plt2.close()
# plt2.clf()
plt2.plot(en, sdosup, "r", linewidth=3, label="s")
plt2.plot(en, -sdosdn, "r", linewidth=3)
plt2.plot(en, pdosup, "g", linewidth=3, label="p")
plt2.plot(en, -pdosdn, "g", linewidth=3)
plt2.plot(en, ddosup, "b", linewidth=3, label="d")
plt2.plot(en, -ddosdn, "b", linewidth=3)
plt2.xlabel("Energies (eV)")
plt2.ylabel("Orb. DOS (arb. unit.)")
plt2.legend(prop={"size": 26})
plt2.xlim(low_lim, up_lim)
plt2.tight_layout()
if plot == True:
tmp = str(filename) + str("/Dos") + str(extra) + str(".png")
plt2.savefig(tmp)
plt3 = get_publication_quality_plot(14, 10)
# plt3.close()
# plt3.clf()
elt_dos = complete_dos.get_element_dos()
at_symbs = set(run.atomic_symbols)
for i, sym in enumerate(at_symbs):
elt = elt_dos[Element(sym)]
# color = cmap(float(i)/len(at_symbs))
if i == 0:
color = "b"
elif i == 1:
color = "g"
elif i == 2:
color = "r"
elif i == 3:
color = "c"
elif i == 4:
color = "m"
elif i == 5:
color = "y"
elif i == 6:
color = "k"
else:
color = "k"
print("Use different color scheme")
plt3.plot(en, elt.densities[Spin.up], color=color, linewidth=3, label=sym)
plt3.plot(en, -elt.densities[Spin.down], color=color, linewidth=3)
plt3.xlabel("Energies (eV)")
plt3.ylabel("Elm. DOS (arb. unit.)")
plt3.legend(prop={"size": 26})
plt3.xlim(low_lim, up_lim)
plt3.tight_layout()
if plot == True:
tmp = str(filename) + str("/EDos") + str(extra) + str(".png")
plt3.savefig(tmp)
return plt1, plt2, plt3
def IP_optics(vrun="", filename=".", extra="", plot=False):
"""
Optoelectronic properties derived from dielectric function
See http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/optic_handout.pdf
http://www.phys.ufl.edu/~tanner/Wooten-OpticalPropertiesOfSolids-2up.pdf
Args:
vrun: path to vasprun.xml
Reurns:
info: dictionary with optoelectronic information
energy: energy bins generally 0 to 40 eV
real_part: real part of dielectric function
imag_part: imaginary part of dielectric function
absorption: absorption coefficient in cm^-1
TODO: shorten the code with multi-dimensional np array
"""
info = {}
storedir = filename
run = Vasprun(vrun, occu_tol=1e-2)
erange = len(run.dielectric[0])
en = []
realx = []
imagx = []
absorpx = []
refrx = []
reflx = []
eelsx = []
extcx = []
opt_conx = []
realy = []
imagy = []
absorpy = []
refry = []
refly = []
eelsy = []
extcy = []
opt_cony = []
realz = []
imagz = []
absorpz = []
refrz = []
reflz = []
eelsz = []
extcz = []
opt_conz = []
H = 4.13566733 * (10**(-15))
# c0=2.99792458
c0 = 2.99792458 * (math.pow(10, 8))
for i in range(0, erange - 1):
en.append(run.dielectric[0][i])
realx.append(run.dielectric[1][i][0])
imagx.append(run.dielectric[2][i][0])
ab_valx = 1.4142 * ((float(run.dielectric[0][i]) / float(H)) * (float(
math.sqrt(-run.dielectric[1][i][0] + math.sqrt(
(run.dielectric[2][i][0]) * (run.dielectric[2][i][0]) +
(run.dielectric[1][i][0]) *
(run.dielectric[1][i][0])))) / float(float(c0) * 100.0)))
absorpx.append(ab_valx)
refr_valx = float(
math.sqrt((run.dielectric[1][i][0]) +
math.sqrt((run.dielectric[2][i][0]) *
(run.dielectric[2][i][0]) +
(run.dielectric[1][i][0]) *
(run.dielectric[1][i][0])))) / float(1.4142)
refrx.append(refr_valx)
eels_valx = float(
run.dielectric[2][i][0]) / float((run.dielectric[2][i][0]) *
(run.dielectric[2][i][0]) +
(run.dielectric[1][i][0]) *
(run.dielectric[1][i][0]))
eelsx.append(eels_valx)
extc_valx = float(
math.sqrt(-(run.dielectric[1][i][0]) +
math.sqrt((run.dielectric[2][i][0]) *
(run.dielectric[2][i][0]) +
(run.dielectric[1][i][0]) *
(run.dielectric[1][i][0])))) / float(1.4142)
extcx.append(extc_valx)
refl_valx = ((refr_valx - 1) *
(refr_valx - 1) + extc_valx * extc_valx) / (
(refr_valx + 1) *
(refr_valx + 1) + extc_valx * extc_valx)
reflx.append(refl_valx)
opt_valx = (float(float(run.dielectric[0][i]) / float(H)) /
float(4 * math.pi) * (run.dielectric[2][i][0]))
opt_conx.append(opt_valx)
realy.append(run.dielectric[1][i][1])
imagy.append(run.dielectric[2][i][1])
ab_valy = 1.4142 * ((float(run.dielectric[0][i]) / float(H)) * (float(
math.sqrt(-run.dielectric[1][i][1] + math.sqrt(
(run.dielectric[2][i][1]) * (run.dielectric[2][i][1]) +
(run.dielectric[1][i][1]) *
(run.dielectric[1][i][1])))) / float(float(c0) * 100.0)))
absorpy.append(ab_valy)
refr_valy = float(
math.sqrt((run.dielectric[1][i][1]) +
math.sqrt((run.dielectric[2][i][1]) *
(run.dielectric[2][i][1]) +
(run.dielectric[1][i][1]) *
(run.dielectric[1][i][1])))) / float(1.4142)
refry.append(refr_valy)
eels_valy = float(
run.dielectric[2][i][1]) / float((run.dielectric[2][i][1]) *
(run.dielectric[2][i][1]) +
(run.dielectric[1][i][1]) *
(run.dielectric[1][i][1]))
eelsy.append(eels_valy)
extc_valy = float(
math.sqrt(-(run.dielectric[1][i][1]) +
math.sqrt((run.dielectric[2][i][1]) *
(run.dielectric[2][i][1]) +
(run.dielectric[1][i][1]) *
(run.dielectric[1][i][1])))) / float(1.4142)
extcy.append(extc_valy)
refl_valy = ((refr_valy - 1) *
(refr_valy - 1) + extc_valy * extc_valy) / (
(refr_valy + 1) *
(refr_valy + 1) + extc_valy * extc_valy)
refly.append(refl_valy)
opt_valy = (float(float(run.dielectric[0][i]) / float(H)) /
float(4 * math.pi) * (run.dielectric[2][i][1]))
opt_cony.append(opt_valy)
realz.append(run.dielectric[1][i][2])
imagz.append(run.dielectric[2][i][2])
ab_valz = 1.4142 * ((float(run.dielectric[0][i]) / float(H)) * (float(
math.sqrt(-run.dielectric[1][i][2] + math.sqrt(
(run.dielectric[2][i][2]) * (run.dielectric[2][i][2]) +
(run.dielectric[1][i][2]) *
(run.dielectric[1][i][2])))) / float(float(c0) * 100.0)))
absorpz.append(ab_valz)
refr_valz = float(
math.sqrt((run.dielectric[1][i][2]) +
math.sqrt((run.dielectric[2][i][2]) *
(run.dielectric[2][i][2]) +
(run.dielectric[1][i][2]) *
(run.dielectric[1][i][2])))) / float(1.4142)
refrz.append(refr_valz)
eels_valz = float(
run.dielectric[2][i][2]) / float((run.dielectric[2][i][2]) *
(run.dielectric[2][i][2]) +
(run.dielectric[1][i][2]) *
(run.dielectric[1][i][2]))
eelsz.append(eels_valz)
extc_valz = float(
math.sqrt(-(run.dielectric[1][i][2]) +
math.sqrt((run.dielectric[2][i][2]) *
(run.dielectric[2][i][2]) +
(run.dielectric[1][i][2]) *
(run.dielectric[1][i][2])))) / float(1.4142)
extcz.append(extc_valz)
refl_valz = ((refr_valz - 1) *
(refr_valz - 1) + extc_valz * extc_valz) / (
(refr_valz + 1) *
(refr_valz + 1) + extc_valz * extc_valz)
reflz.append(refl_valz)
opt_valz = (float(float(run.dielectric[0][i]) / float(H)) /
float(4 * math.pi) * (run.dielectric[2][i][2]))
opt_conz.append(opt_valz)
if plot == True:
# plt.close()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, realx, linewidth=2, label=r"$\epsilon_1x$")
plt.plot(en, realy, linewidth=2, label=r"$\epsilon_1y$")
plt.plot(en, realz, linewidth=2, label=r"$\epsilon_1z$")
plt.legend(prop={"size": 26})
plt.xlim([0, 30])
plt.xlabel("Energy (eV)")
plt.ylabel("Dielec. function (Real part)")
filename = str(storedir) + str("/") + str("Real") + str(extra) + str(
".png")
plt.tight_layout()
plt.savefig(filename)
plt.tight_layout()
plt.close()
plt.clf()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, imagx, linewidth=2, label=r"$\epsilon_2x$")
plt.plot(en, imagy, linewidth=2, label=r"$\epsilon_2y$")
plt.plot(en, imagz, linewidth=2, label=r"$\epsilon_2z$")
plt.xlabel("Energy (eV)")
plt.xlim([0, 30])
plt.ylabel("Dielec. function(Imag part)")
filename = str(storedir) + str("/") + str("Imag") + str(extra) + str(
".png")
plt.tight_layout()
plt.legend(prop={"size": 26})
plt.savefig(filename)
plt.close()
plt.clf()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, refrx, linewidth=2, label=r"$n_x$")
plt.plot(en, refry, linewidth=2, label=r"$n_y$")
plt.plot(en, refrz, linewidth=2, label=r"$n_z$")
plt.xlim([0, 30])
plt.xlabel("Energy (eV)")
plt.ylabel("Refractive index")
filename = str(storedir) + str("/") + str("Refr") + str(extra) + str(
".png")
plt.tight_layout()
plt.legend(prop={"size": 26})
plt.savefig(filename)
plt.close()
plt.clf()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, extcx, linewidth=2, label=r"$k_x$")
plt.plot(en, extcy, linewidth=2, label=r"$k_y$")
plt.plot(en, extcz, linewidth=2, label=r"$k_z$")
plt.xlim([0, 30])
plt.xlabel("Energy (eV)")
plt.ylabel("Extinction Coefficient")
filename = str(storedir) + str("/") + str("Extc") + str(extra) + str(
".png")
plt.tight_layout()
plt.legend(prop={"size": 26})
plt.savefig(filename)
plt.tight_layout()
plt.close()
plt.clf()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, absorpx, linewidth=2, label=r"$\alpha_x$")
plt.plot(en, absorpy, linewidth=2, label=r"$\alpha_y$")
plt.plot(en, absorpz, linewidth=2, label=r"$\alpha_z$")
plt.xlim([0, 30])
plt.xlabel("Energy (eV)")
plt.ylabel("Absorption coefficient")
filename = str(storedir) + str("/") + str("Absorp") + str(extra) + str(
".png")
plt.tight_layout()
plt.legend(prop={"size": 26})
plt.savefig(filename)
plt.tight_layout()
plt.close()
plt.clf()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, eelsx, linewidth=2, label=r"$e_x$")
plt.plot(en, eelsy, linewidth=2, label=r"$e_y$")
plt.plot(en, eelsz, linewidth=2, label=r"$e_z$")
plt.xlim([0, 30])
plt.xlabel("Energy (eV)")
plt.ylabel("Energy loss spectrum")
filename = str(storedir) + str("/") + str("ELS") + str(extra) + str(
".png")
plt.tight_layout()
plt.legend(prop={"size": 26})
plt.savefig(filename)
plt.tight_layout()
plt.close()
plt.clf()
plt = get_publication_quality_plot(14, 10)
plt.plot(en, opt_conx, linewidth=2, label=r"$\sigma_x$")
plt.plot(en, opt_cony, linewidth=2, label=r"$\sigma_y$")
plt.plot(en, opt_conz, linewidth=2, label=r"$\sigma_z$")
plt.xlim([0, 30])
plt.xlabel("Energy (eV)")
plt.ylabel("Optical conductivity (Real part)")
filename = str(storedir) + str("/") + str("Opt_con") + str(
extra) + str(".png")
plt.tight_layout()
plt.legend(prop={"size": 26})
plt.savefig(filename)
plt.tight_layout()
plt.close()
info["absorption"] = [absorpx, absorpy, absorpz]
info["energy"] = en
info["real_part"] = [realx, realy, realz]
info["imag_part"] = [imagx, imagy, imagz]
info["refr_index"] = [refrx, refry, refrz]
info["extinc"] = [extcx, extcy, extcz]
info["reflectance"] = [reflx, refly, reflz]
info["EELS"] = [eelsx, eelsy, eelsz]
info["opt_conduct"] = [opt_conx, opt_cony, opt_conz]
print(info["real_part"][0][0])
return info